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Integrative metabolic engineering

1 Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA;
2 Dept. of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, USA

Special Issues: Recent Advances in Metabolic Engineering

Recent advances in experimental and computational synthetic biology are extremely useful for achieving metabolic engineering objectives. The integration of synthetic biology and metabolic engineering within an iterative design-build-test framework will improve the practice of metabolic engineering by relying more on efficient design strategies. Computational tools that aid in the design and in silico simulation of metabolic pathways are especially useful. However, software helpful for constructing, implementing, measuring and characterizing engineered pathways and networks should not be overlooked. In this review, we highlight computational synthetic biology tools relevant to metabolic engineering, organized in the context of the design-build-test cycle.
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References

1. Stephanopoulos G (2012) Synthetic Biology and Metabolic Engineering. ACS Synth Biol 1: 514-525.    

2. Klein-Marcuschamer D, Yadav VG, Ghaderi A, et al. (2010) De novo metabolic engineering and the promise of synthetic DNA. Adv Biochem Eng Biotechnol 120: 101-131.

3. Yadav VG, Stephanopoulos G (2010) Reevaluating synthesis by biology. Curr Opin Microbiol 1-6.

4. Nielsen J, Fussenegger M, Keasling J, et al. (2014) Engineering synergy in biotechnology. Nature Publishing Group 10: 319-322.

5. Church GM, Elowitz MB, Smolke CD, et al. (2014) Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 15: 289-294.    

6. Bayer TS (2010) Transforming biosynthesis into an information science. Nat Chem Biol 6: 859-861.    

7. Yeh BJ, Lim WA (2007) Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 3: 521-525.    

8. Keasling JD (2010) Manufacturing Molecules Through Metabolic Engineering. Science 330: 1355-1358.    

9. McArthur IV GH, Fong SS (2010) Toward Engineering Synthetic Microbial Metabolism. J Biomed Biotechnol 2010: 1-10.

10. Lee JW, Na D, Park JM, et al. (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8: 536-546.    

11. Fong SS (2014) Computational approaches to metabolic engineering utilizing systems biology and synthetic biology. CSBJ 11: 28-34.    

12. Smolke CD (2009) Building outside of the box: iGEM and the BioBricks Foundation. Nat Biotechnol 27: 1099-1102.    

13. Ham TS, Dmytriv Z, Plahar H, et al. (2012) Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res 40: e141-e141.    

14. Mutalik VK, Guimaraes JC, Cambray G, et al. (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 1-15.

15. Adames NR, Wilson ML, Fang G, et al. (2015) GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Res.

16. Weber T, Blin K, Duddela S, et al. (2015) antiSMASH 3.0--a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res.

17. Hsiau TH-C, Anderson JC (2014) Engineered DNA Sequence Syntax Inspector. ACS Synth Biol 3: 91-96.    

18. Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27: 946-950.    

19. Casini A, Christodoulou G, Freemont PS, et al. (2014) R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences. ACS Synth Biol 3: 525-528.    

20. Siegel JB, Smith AL, Poust S, et al. (2015) Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci USA 112: 3704-3709.

21. Chappell J, Takahashi MK, Lucks JB (2015) Creating small transcription activating RNAs. Nat Chem Biol 11: 214-220.    

22. Stevens JT, Carothers JM (2015) Designing RNA-Based Genetic Control Systems for Efficient Production from Engineered Metabolic Pathways. ACS Synth Biol 4: 107-115.    

23. Carothers JM, Goler JA, Juminaga D, et al. (2011) Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression. Science 334: 1716-1719.    

24. Oberortner E, Densmore D (2014) Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems. ACS Synth Biol 141216122616002.

25. Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD. Nucleic Acids Res 37: W40-W47.    

26. Smanski MJ, Bhatia S, Zhao D, et al. (2014) Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol 32: 1241-1249.    

27. Purcell O, Peccoud J, Lu TK (2014) Rule-Based Design of Synthetic Transcription Factors in Eukaryotes. ACS Synth Biol 3: 737-744.    

28. Kaznessis YN (2011) SynBioSS-Aided Design of Synthetic Biological Constructs, 1st ed., vol. 498. Elsevier Inc. 137-152.

29. Myers CJ, Barker N, Jones K, et al. (2009) iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 25: 2848-2849.    

30. Hillson NJ, Rosengarten RD, Keasling JD (2012) j5 DNA Assembly Design Automation Software. ACS Synth Biol 1: 14-21.    

31. Gibson DG, Young L, Chuang R-Y, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6: 343-345.    

32. Gibson DG, Smith HO, Hutchison CA, et al. (2010) Chemical synthesis of the mouse mitochondrial genome. Nat Methods 7: 901-903.    

33. Richardson SM, Nunley PW, Yarrington RM, et al. (2010) GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res 38: 2603-2606.

34. Jakočiūnas T, Bonde I, Herrgård M, et al. (2015) Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 28: 213-222.    

35. Wang HH, Isaacs FJ, Carr PA, et al. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 1-6.

36. Wang HH, Kim H, Cong L, et al. (2012) Genome-scale promoter engineering by coselection MAGE. Nat Methods 9: 591-593.    

37. Hsu PD, Scott DA, Weinstein JA, et al. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827-832.    

38. Montague TG, Cruz JM, Gagnon JA, et al. (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42: W401-W407.    

39. Doench JG, Hartenian E, Graham DB, et al. (2014) Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 1-8.

40. Bonde MT, Klausen MS, Anderson MV, et al. (2014) MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res 42: W408-W415.    

41. Untergasser A, Nijveen H, Rao X, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-W74.    

42. Wilson ML, Cai Y, Hanlon R, et al. (2012) Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic Acids Res 41: e25-e25.

43. O'Brien EJ, Lerman JA, Chang RL, et al. (2013) Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 9: 1-13.

44. Ball DA, Lux MW, Adames NR, et al. (2014) Adaptive Imaging Cytometry to Estimate Parameters of Gene Networks Models in Systems and Synthetic Biology. PLoS ONE 9: e107087.    

45. Beal J, Weiss R, Densmore D, et al. (2012) An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synth Biol 1: 317-331.    

46. Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26: 787-793.    

47. Endy D (2005) Foundations for engineering biology. Nature 438: 449-453.    

48. Fisher AB, Canfield ZB, Hayward LC, et al. (2013) Ex vivo DNA assembly. Front Bioeng Biotechnol 1: 1-7.

49. Galdzicki M, Clancy KP, Oberortner E, et al. (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol 32: 545-550.    

50. Chan LY, Kosuri S, Endy D, et al. (2005) Refactoring bacteriophage T7. Mol Syst Biol 1: 0018.

51. Temme K, Zhao D, Voigt CA (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. P Natl Acad Sci U S A 109: 7085-7090.    

52. Yadav VG, De May M, Lim CG, et al. (2012) The Future of Metabolic Engineering and Synthetic Biology: Towards a Systematic Practice. Metab Eng 14: 233-241.    

Copyright Info: © 2015, Stephen S Fong, et al., licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (http://creativecommons.org/licenses/by/4.0)

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